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Commit 35d5e2ec authored by Rachel Clipp's avatar Rachel Clipp
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Merge branch 'feature/documentation' of... 

Merge branch 'feature/documentation' of https://gitlab.kitware.com/physiology/engine into feature/documentation
parents e5b500f5 eec1b8ca
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.gitignore
View file @ 35d5e2ec
......@@ -9,10 +9,10 @@
src/schema/schema_last_built
/src/cpp/bind
/src/csharp/pulse/bind
/src/java/com
/src/java/pulse/cdm/bind
/src/java/pulse/cpm/bind
/src/java/pulse/study/bind
/src/java/com/google
/src/java/com/kitware/pulse/cdm/bind
/src/java/com/kitware/pulse/cpm/bind
/src/java/com/kitware/pulse/study/bind
/src/python/pulse/cdm/bind
/src/python/pulse/cpm/bind
/src/python/pulse/study/bind
......
bin/run.cmake.in
View file @ 35d5e2ec
# Scripts to assist developers
# Mostly these are calling the test suite driver and validator classes in Java
# TODO More Test Targets
# Rebasing
# com.kitware.physiology.utilities.testing.Rebase [from to (config|ALL)]
#
# Ploting
# com.kitware.physiology.utilities.csv.plots.PlotDriver
#
# Reconfigure the config file (in memory) so we can test serialization
# com.kitware.physiology.utilities.testing.Reconfiguration
find_package(Java REQUIRED)
include(UseJava)
......@@ -23,24 +14,19 @@ endif()
#set(Java_JAVA_EXECUTABLE "/the_jdk_I_want/bin/java)
set(JAVA_CLASSPATH Pulse.jar
"@CMAKE_SOURCE_DIR@/src/java/jar/javassist-3.16.1-GA.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jcommon-1.0.16.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jdom-2.0.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jfreechart-1.0.13.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/gson-2.8.5.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/guava-26.0-jre.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/log4j-1.2.17.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-3.13-20150929.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-3.13-20150929.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-schemas-3.13-20150929.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/pdfbox-2.0.0-RC3.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/reflections-0.9.9-RC1-uberjar.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/xmlbeans-2.6.0.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/zip4j-1.3.1.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/org.eclipse.jgit-4.11.0.201803080745-r.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/slf4j-api-1.7.25.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/slf4j-simple-1.7.25.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/error_prone_annotations-2.3.2.jar")
"@CMAKE_SOURCE_DIR@/src/java/jar/commons-collections4-4.4.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/commons-compress-1.19.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/commons-math3-3.6.1.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/error_prone_annotations-2.3.4.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/gson-2.8.6.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/guava-29.0-jre.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jfreechart-1.5.0.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/javassist.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-4.1.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-4.1.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-schemas-4.1.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/reflections-0.9.12.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/xmlbeans-3.1.0.jar")
if(NOT WIN32)
string(REPLACE ";" ":" JAVA_CLASSPATH "${JAVA_CLASSPATH}")
......@@ -48,22 +34,22 @@ endif()
if(TYPE STREQUAL "tests" OR TYPE STREQUAL "SystemValidation" OR TYPE STREQUAL "PatientValidation")
if(TYPE STREQUAL "tests")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver CDMUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver EngineUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver ScenarioVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver CDMUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver EngineUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver ScenarioVerification.config)
endif()
if(TYPE STREQUAL "SystemValidation" OR TYPE STREQUAL "tests")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver SystemVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.SystemValidation TEST)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver SystemVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.SystemValidation TEST)
endif()
if(TYPE STREQUAL "PatientValidation" OR TYPE STREQUAL "tests")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver PatientVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.PatientValidation TEST)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver PatientVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.PatientValidation TEST)
endif()
elseif(TYPE STREQUAL "genData")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.dataset.DataSetReader)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.dataset.DataSetReader)
elseif(TYPE STREQUAL "genStates")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver InitialPatientStates.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver InitialPatientStates.config)
elseif(TYPE STREQUAL "doxygen")
file(READ @CMAKE_SOURCE_DIR@/docs/Doxygen/header.html HEADER)
file(READ @CMAKE_SOURCE_DIR@/docs/Doxygen/footer.html FOOTER)
......@@ -90,13 +76,13 @@ elseif(TYPE STREQUAL "doxygen")
file(WRITE @CMAKE_SOURCE_DIR@/docs/Doxygen/panel_footer.html "${FOOTER_PANEL}")
file(APPEND @CMAKE_SOURCE_DIR@/docs/Doxygen/panel_footer.html "${FOOTER}")
# These are run above
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.SystemValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.PatientValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Markdown" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Methodology" ./docs/markdown ./test_results/tables)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.Proto2Doxygen "@CMAKE_SOURCE_DIR@/src/schema" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.CDM2MD ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.utilities.csv.plots.PlotDriver PlotRun.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.SystemValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.PatientValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Markdown" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Methodology" ./docs/markdown ./test_results/tables)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.Proto2Doxygen "@CMAKE_SOURCE_DIR@/src/schema" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.CDM2MD ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.PlotDriver PlotRun.config)
execute_process(COMMAND doxygen ./docs/full.doxy)
# Build our landing files
setup_landing_page(index.html)
......@@ -112,16 +98,30 @@ elseif(TYPE STREQUAL "protoc")
-P "@CMAKE_SOURCE_DIR@/src/schema/GenerateBindings.cmake")
elseif(TYPE STREQUAL "updateBaselines")
execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@" --target UpdateVerification)
elseif(TYPE STREQUAL "jar")
execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@" --target PulseJava)
elseif(TYPE STREQUAL "rebase")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.Rebase)
# find Git and if available set GIT_HASH variable
find_package(Git QUIET)
if(GIT_FOUND)
execute_process(
COMMAND ${GIT_EXECUTABLE} log -1 --pretty=format:%h
OUTPUT_VARIABLE GIT_HASH
OUTPUT_STRIP_TRAILING_WHITESPACE
ERROR_QUIET
WORKING_DIRECTORY
@CMAKE_SOURCE_DIR@
)
endif()
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.Rebase ${GIT_HASH})
elseif(TYPE STREQUAL "FullReport")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SEReportResults)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SEReportResults)
elseif(TYPE STREQUAL "plotter")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.utilities.csv.plots.CSVPlotTool ${ARG1})
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.CSVPlotTool ${ARG1})
else()
if(${TYPE} MATCHES "Plot")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.utilities.csv.plots.PlotDriver ${TYPE}.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.PlotDriver ${TYPE}.config)
else()
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver ${TYPE}.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver ${TYPE}.config)
endif()
endif()
data/config/CDMUnitTests.config
View file @ 35d5e2ec
......@@ -14,7 +14,7 @@ PlotResults=true
PercentDifference=2.0
Threads=-1
Executor=pulse.cdm.testing.CDMUnitTestDriver
Executor=com.kitware.pulse.cdm.testing.CDMUnitTestDriver
Macro CDMUnitTest=CDMUnitTestDriver FastPlotErrors Baseline=unit_tests/cdm/ Computed=./test_results/unit_tests/cdm/
@group Simple Circuits
......
data/config/DebugPlots.config
View file @ 35d5e2ec
......@@ -49,11 +49,11 @@
# FLAGS FOR RESPIRATORY PFT PLOTTER ONLY
# PFTFile - Specify the path and filename for the .pba containing the PFT data you want to plot (No spaces allowed)
Plotter=pulse.utilities.csv.plots.ActionEventPlotter
Plotter=pulse.utilities.csv.plots.MultiPlotter
Plotter=pulse.utilities.csv.plots.ConvexHullPlotter
Plotter=pulse.utilities.csv.plots.RespiratoryPFTPlotter
Plotter=pulse.utilities.csv.plots.MultiSourcePlotter
Plotter=com.kitware.pulse.utilities.csv.plots.ActionEventPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.MultiPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.ConvexHullPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.RespiratoryPFTPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.MultiSourcePlotter
#ScenarioName=PlotterType Flag1=Stuff Flag2=Stuff Flag3 FlagN
......@@ -63,3 +63,4 @@ Plotter=pulse.utilities.csv.plots.MultiSourcePlotter
#RespiratoryValidation=RespiratoryPFTPlotter Header=TotalLungVolume(mL) VerificationDir=validation/systems/ PFTFile=RespiratoryValidationPFT@120.02s.json Title=Pulmonary_Function_Test_Results OutputOverride=./docs/html/plots/Respiratory/
CardiacShock=MultiPlotter Title=Cardiovascular_Response_To_Hemorrhage PercentOfBaseline X1Label=Percent_Of_Blood_Loss X1=BloodVolume(L) Y1=CardiacOutput(L/min) Y1LowerBound=0 X2=BloodVolume(L) Y2=MeanArterialPressure(mmHg) Y2LowerBound=0 X1LowerBound=0 X1UpperBound=50 DataPathVerificationOverride=scenarios/patient/ Title=None DataFileOverride=HemorrhageClass4NoFluidResults.csv OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=CardiacShock.jpg
HemorrhageGroups=MultiSourcePlotter Title=Cardiovascular_Hemorrhage_Groups PercentOfBaseline X1=Time(s) Y1=MeanArterialPressure(mmHg) Y1Label=Mean_Arterial_Pressure_Delta Y1LowerBound=0 Y1UpperBound=100 DataPathVerificationOverride=scenarios/patient/ Title=None DataFileOverride=HemorrhageGroup1Results.csv,HemorrhageGroup2Results.csv,HemorrhageGroup3Results.csv,HemorrhageGroup4Results.csv,HemorrhageGroup5Results.csv,HemorrhageGroup6Results.csv OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=HemorrhageGroups.jpg
HemorrhageClass3NoFluid=ActionEventPlotter LegendOnly ActionsOnly Header=RightAfferentArterioleResistance(mmHg_min/mL) Title=HemorrhageClass4NoFluidLegend VerificationDir=patient OutputOverride=./docs/html/plots/Renal/ NoEvents ImageDimensions=1500,160
data/config/DebugRun.config
View file @ 35d5e2ec
......@@ -22,9 +22,9 @@ Threads=-1
# Time stamp periods is creating a file per save and using the time stamp as naming convention
#AutoSerialization=./states/testing/,5,On,On,On
Executor=pulse.cdm.testing.CDMUnitTestDriver
Executor=pulse.engine.testing.EngineUnitTestDriver
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.cdm.testing.CDMUnitTestDriver
Executor=com.kitware.pulse.engine.testing.EngineUnitTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro CDMUnitTest=CDMUnitTestDriver FastPlotErrors Baseline=unit_tests/cdm/ Computed=./test_results/unit_tests/cdm
Macro EngineUnitTest=EngineUnitTestDriver FastPlot Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse
......
data/config/DrugPKVerification.config
View file @ 35d5e2ec
......@@ -20,7 +20,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/config/EngineUnitTests.config
View file @ 35d5e2ec
......@@ -14,7 +14,7 @@ PlotResults=true
PercentDifference=2.0
Threads=-1
Executor=pulse.engine.testing.EngineUnitTestDriver
Executor=com.kitware.pulse.engine.testing.EngineUnitTestDriver
Macro EngineUnitTest=EngineUnitTestDriver FastPlotErrors Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse/
Macro FullPlotEngineUnitTest=EngineUnitTestDriver FullPlotErrors Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse/
......@@ -23,9 +23,10 @@ ReadScenarios = EngineUnitTestDriver NoCompare Computed=./test_results/unit_test
@group Cardiovascular
CardiovascularCircuitAndTransport = EngineUnitTest Results=CardiovascularCircuitOutput,CardiovascularTransportOutput
CardiovascularAndCerebrospinalFluidCircuitAndTransport = EngineUnitTest Results=CardiovascularAndCerebrospinalFluidCircuitOutput,CardiovascularAndCerebrospinalFluidTransportOutput
CardiovascularAndRenalCircuitAndTransport = EngineUnitTest Results=CardiovascularAndRenalCircuitOutput,CardiovascularAndRenalTransportOutput
CardiovascularAndTissueCircuitAndTransport = EngineUnitTest Results=CardiovascularAndTissueCircuitOutput,CardiovascularAndTissueTransportOutput
CardiovascularTissueAndRenalCircuitAndTransport = EngineUnitTest Results=CardiovascularTissueAndRenalCircuitOutput,CardiovascularTissueAndRenalTransportOutput
FullCardiovascularCircuitAndTransport = EngineUnitTest Results=FullCardiovascularCircuitOutput,FullCardiovascularTransportOutput
CardiovascularBloodGases = EngineUnitTest Results=CardiovascularBloodGasesTestCircuitOutput,CardiovascularBloodGasesTestTransportOutput
TuneCardiovascularCircuit = EngineUnitTest NoCompare
......
data/config/InitialPatientStates.config
View file @ 35d5e2ec
......@@ -16,7 +16,7 @@ Patients=all
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioRun=ScenarioTestDriver NoPlot Scenario=./ Computed=./test_results/scenarios/
......
data/config/LongVerificationScenarios.config
View file @ 35d5e2ec
......@@ -22,7 +22,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/config/PatientVerification.config
View file @ 35d5e2ec
......@@ -16,7 +16,7 @@ Patients=all
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/config/PlotRun.config
View file @ 35d5e2ec
......@@ -50,11 +50,11 @@
# FLAGS FOR RESPIRATORY PFT PLOTTER ONLY
# PFTFile - Specify the path and filename for the .xml containing the PFT data you want to plot (No spaces allowed)
Plotter=pulse.utilities.csv.plots.ActionEventPlotter
Plotter=pulse.utilities.csv.plots.MultiPlotter
Plotter=pulse.utilities.csv.plots.ConvexHullPlotter
Plotter=pulse.utilities.csv.plots.RespiratoryPFTPlotter
Plotter=pulse.utilities.csv.plots.MultiSourcePlotter
Plotter=com.kitware.pulse.utilities.csv.plots.ActionEventPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.MultiPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.ConvexHullPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.RespiratoryPFTPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.MultiSourcePlotter
########## Physiologic Systems ##########
......@@ -355,6 +355,12 @@ MechanicalVentilatorPressureControlledVaried=ActionEventPlotter NoGrid Header=Ti
MechanicalVentilatorPressureControlledVaried=ActionEventPlotter NoGrid Header=InspiratoryExpiratoryRatio VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents RemoveLegends OutputFilename=MechanicalVentilatorPressureControlledVaried_InspiratoryExpiratoryRatio.jpg
MechanicalVentilatorPressureControlledVaried=ActionEventPlotter Header=TidalVolume(mL) VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents LegendOnly Title=MechanicalVentilatorPressureControlledVariedLegend ImageDimensions=1800,820
MechanicalVentilatorVolumeControlledARDS=ActionEventPlotter NoGrid Header=TotalLungVolume(L) VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents RemoveLegends OutputFilename=MechanicalVentilatorVolumeControlledARDS_TotalLungVolume.jpg
MechanicalVentilatorVolumeControlledARDS=ActionEventPlotter NoGrid Header=RespirationRate(1/min) VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents RemoveLegends OutputFilename=MechanicalVentilatorVolumeControlledARDS_RR.jpg
MechanicalVentilatorVolumeControlledARDS=ActionEventPlotter NoGrid Header=TidalVolume(mL) VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents RemoveLegends OutputFilename=MechanicalVentilatorVolumeControlledARDS_TidalVolume.jpg
MechanicalVentilatorVolumeControlledARDS=ActionEventPlotter NoGrid Header=InspiratoryExpiratoryRatio VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents RemoveLegends OutputFilename=MechanicalVentilatorVolumeControlledARDS_InspiratoryExpiratoryRatio.jpg
MechanicalVentilatorVolumeControlledARDS=ActionEventPlotter Header=TidalVolume(mL) VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents LegendOnly Title=MechanicalVentilatorVolumeControlledARDSLegend ImageDimensions=1800,820
MechanicalVentilatorPressureControlledARDS=ActionEventPlotter NoGrid Header=TidalVolume(mL) VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents RemoveLegends OutputFilename=MechanicalVentilatorPressureControlledARDS_TidalVolume.jpg
MechanicalVentilatorPressureControlledARDS=ActionEventPlotter NoGrid Header=OxygenSaturation VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents RemoveLegends OutputFilename=MechanicalVentilatorPressureControlledARDS_OxygenSaturation.jpg
MechanicalVentilatorPressureControlledARDS=ActionEventPlotter NoGrid Header=CarricoIndex(mmHg) VerificationDir=equipment OutputOverride=./docs/html/plots/MechanicalVentilator/ NoEvents RemoveLegends OutputFilename=MechanicalVentilatorPressureControlledARDS_CarricoIndex.jpg
......
data/config/ScenarioVerification.config
View file @ 35d5e2ec
......@@ -22,7 +22,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......@@ -125,6 +125,7 @@ equipment/MainstemIntubation.json = ScenarioTest
equipment/MechanicalVentilation.json = ScenarioTest
equipment/MechanicalVentilatorPressureControlledARDS.json = ScenarioTest
equipment/MechanicalVentilatorPressureControlledVaried.json = ScenarioTest
equipment/MechanicalVentilatorVolumeControlledARDS.json = ScenarioTest
equipment/NasalCannula.json = ScenarioTest
equipment/NonRebreatherMask.json = ScenarioTest
equipment/SimpleMask.json = ScenarioTest
......
data/config/SystemVerification.config
View file @ 35d5e2ec
......@@ -16,7 +16,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/human/adult/scenarios/equipment/MechanicalVentilatorPressureControlledARDS.json
View file @ 35d5e2ec
......@@ -115,7 +115,7 @@
"ExpirationWaveform": "Square",
"PeakInspiratoryPressure": { "ScalarPressure": { "Value": 20.0, "Unit": "cmH2O" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 8.0, "Unit": "cmH2O" } },
"InspirationTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"ExpirationCycleTime": { "ScalarTime": { "Value": 1.0, "Unit": "s" } },
"FractionInspiredGas": [
{ "Name": "Oxygen", "Amount": { "Scalar0To1": { "Value": 0.25, "Unit": "" } } }
......@@ -147,7 +147,7 @@
"ExpirationWaveform": "Square",
"PeakInspiratoryPressure": { "ScalarPressure": { "Value": 25.0, "Unit": "cmH2O" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 10.0, "Unit": "cmH2O" } },
"InspirationTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"ExpirationCycleTime": { "ScalarTime": { "Value": 1.0, "Unit": "s" } },
"FractionInspiredGas": [
{ "Name": "Oxygen", "Amount": { "Scalar0To1": { "Value": 0.5, "Unit": "" } } }
......@@ -179,7 +179,7 @@
"ExpirationWaveform": "Square",
"PeakInspiratoryPressure": { "ScalarPressure": { "Value": 32.0, "Unit": "cmH2O" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 15.0, "Unit": "cmH2O" } },
"InspirationTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"ExpirationCycleTime": { "ScalarTime": { "Value": 1.0, "Unit": "s" } },
"FractionInspiredGas": [
{ "Name": "Oxygen", "Amount": { "Scalar0To1": { "Value": 0.9995, "Unit": "" } } }
......
data/human/adult/scenarios/equipment/MechanicalVentilatorPressureControlledVaried.json
View file @ 35d5e2ec
......@@ -109,7 +109,7 @@
"ExpirationWaveform": "Square",
"PeakInspiratoryPressure": { "ScalarPressure": { "Value": 10.0, "Unit": "cmH2O" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 5.0, "Unit": "cmH2O" } },
"InspirationTriggerTime": { "ScalarTime": { "Value": 3.33, "Unit": "s" } },
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 3.33, "Unit": "s" } },
"ExpirationCycleTime": { "ScalarTime": { "Value": 1.67, "Unit": "s" } },
"FractionInspiredGas": [
{ "Name": "Nitrogen", "Amount": { "Scalar0To1": { "Value": 0.7896, "Unit": "" } } },
......@@ -137,7 +137,7 @@
"ExpirationWaveform": "Square",
"PeakInspiratoryPressure": { "ScalarPressure": { "Value": 20.0, "Unit": "cmH2O" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 10.0, "Unit": "cmH2O" } },
"InspirationTriggerTime": { "ScalarTime": { "Value": 1.5, "Unit": "s" } },
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 1.5, "Unit": "s" } },
"ExpirationCycleTime": { "ScalarTime": { "Value": 1.5, "Unit": "s" } },
"FractionInspiredGas": [
{ "Name": "Oxygen", "Amount": { "Scalar0To1": { "Value": 0.3, "Unit": "" } } } ],
......
data/human/adult/scenarios/equipment/MechanicalVentilatorVolumeControlledARDS.json 0 → 100644
View file @ 35d5e2ec
{
"Name": "MechanicalVentilatorVolumeControlledARDS",
"Description": "Apply a VC-AC mode ventilator to treat a patient with ARDS.",
"PatientConfiguration": { "PatientFile": "StandardMale.json",
"Conditions": { "AnyCondition": [ {
"PatientCondition": {
"AcuteRespiratoryDistressSyndrome": {
"Severity": { "Scalar0To1": { "Value": 0.6 } },
"LeftLungAffected": { "Scalar0To1": { "Value": 1.0 } },
"RightLungAffected": { "Scalar0To1": { "Value": 1.0 } } } } }
] }
},
"DataRequestManager":
{
"DataRequest":
[
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{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "HeartRate", "Unit": "1/min" },
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{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "ArterialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "MeanArterialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { }, "Category": "Physiology", "PropertyName": "SystolicArterialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "DiastolicArterialPressure", "Unit": "mmHg" },
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{ "DecimalFormat": { }, "Category": "Physiology", "PropertyName": "HemoglobinContent", "Unit": "g" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "CentralVenousPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "PulmonaryCapillariesWedgePressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TidalVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "TotalLungVolume", "Unit": "L" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "RespirationRate", "Unit": "1/min" },
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]
},
"AnyAction":
[
{ "AdvanceTime": { "Time": { "ScalarTime": { "Value": 30.0, "Unit": "s" } } } },
{ "PatientAction": { "Intubation": { "Type": "Tracheal" } } },
{
"EquipmentAction": {
"MechanicalVentilatorConfiguration": {
"MechanicalVentilatorAction": { "EquipmentAction": { "Action": {
"Comment": "Attach the mechanical ventilator" }}},
"Configuration":
{
"Connection": "Tube",
"InspirationWaveform": "Square",
"ExpirationWaveform": "Square",
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 5.0, "Unit": "s" } },
"InspirationPatientTriggerPressure": { "ScalarPressure": { "Value": -0.000001, "Unit": "cmH2O" } },
"InspirationTargetFlow": { "ScalarVolumePerTime": { "Value": 0.5, "Unit": "L/s" } },
"ExpirationCycleVolume": { "ScalarVolume": { "Value": 0.540, "Unit": "L" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 8.0, "Unit": "cmH2O" } },
"FractionInspiredGas": [
{ "Name": "Oxygen", "Amount": { "Scalar0To1": { "Value": 0.5, "Unit": "" } } }
]
}
}
}
},
{ "AdvanceTime": { "Time": { "ScalarTime": { "Value": 5.0, "Unit": "min" } } } }
]
}
\ No newline at end of file
data/human/adult/scenarios/showcase/COVID19Ventilation.json
View file @ 35d5e2ec
......@@ -103,7 +103,7 @@
"ExpirationWaveform": "Square",
"PeakInspiratoryPressure": { "ScalarPressure": { "Value": 10.0, "Unit": "cmH2O" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 0.0, "Unit": "cmH2O" } },
"InspirationTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"ExpirationCycleTime": { "ScalarTime": { "Value": 1.0, "Unit": "s" } },
"FractionInspiredGas":
[
......@@ -132,7 +132,7 @@
"ExpirationWaveform": "Square",
"PeakInspiratoryPressure": { "ScalarPressure": { "Value": 30.0, "Unit": "cmH2O" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 12.0, "Unit": "cmH2O" } },
"InspirationTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"ExpirationCycleTime": { "ScalarTime": { "Value": 1.0, "Unit": "s" } },
"FractionInspiredGas":
[
......@@ -172,7 +172,7 @@
"ExpirationWaveform": "Square",
"PeakInspiratoryPressure": { "ScalarPressure": { "Value": 22.0, "Unit": "cmH2O" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 8.0, "Unit": "cmH2O" } },
"InspirationTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"ExpirationCycleTime": { "ScalarTime": { "Value": 1.0, "Unit": "s" } },
"FractionInspiredGas":
[
......@@ -211,7 +211,7 @@
"ExpirationWaveform": "Square",
"PeakInspiratoryPressure": { "ScalarPressure": { "Value": 18.0, "Unit": "cmH2O" } },
"PositiveEndExpiredPressure": { "ScalarPressure": { "Value": 6.0, "Unit": "cmH2O" } },
"InspirationTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"InspirationMachineTriggerTime": { "ScalarTime": { "Value": 2.0, "Unit": "s" } },
"ExpirationCycleTime": { "ScalarTime": { "Value": 1.0, "Unit": "s" } },
"FractionInspiredGas":
[
......
docs/Doxygen/header.html
View file @ 35d5e2ec
......@@ -111,6 +111,7 @@
<li><a href="_renal_methodology.html">Renal</a></li>
<li><a href="_respiratory_methodology.html">Respiratory</a></li>
<li><a href="_tissue_methodology.html">Tissue</a></li>
<li><a href="_mechanical_ventilator_methodology.html">Mechancial Ventilator</a></li>
<li><a href="_anesthesia_machine_methodology.html">Anesthesia Machine</a></li>
<li><a href="_inhaler_methodology.html">Inhaler</a></li>